2HYE

Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery.

Angers, S.Li, T.Yi, X.MacCoss, M.J.Moon, R.T.Zheng, N.

(2006) Nature 443: 590-593

  • DOI: 10.1038/nature05175

  • PubMed Abstract: 
  • Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catal ...

    Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Washington, School of Medicine, Box 357280, Seattle, Washington 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1
A
1140Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nonstructural protein V
B
222Parainfluenza virus 5 (strain W3)Mutation(s): 0 
Gene Names: P/V
Find proteins for P11207 (Parainfluenza virus 5 (strain W3))
Go to UniProtKB:  P11207
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cullin-4A
C
759Homo sapiensMutation(s): 0 
Gene Names: CUL4A
Find proteins for Q13619 (Homo sapiens)
Go to Gene View: CUL4A
Go to UniProtKB:  Q13619
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RING-box protein 1
D
108Homo sapiensMutation(s): 0 
Gene Names: RBX1 (RNF75, ROC1)
EC: 2.3.2.27, 2.3.2.32
Find proteins for P62877 (Homo sapiens)
Go to Gene View: RBX1
Go to UniProtKB:  P62877
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.250 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 83.452α = 90.00
b = 203.165β = 90.00
c = 424.875γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2007-10-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description